I believe there is a clear and present need across all science fields
to make workflows more efficient, improve data management, and make our
results accessible and digestible to general audiences. The first step
toward this is to embrace analysis-to-product workflows in programs like
R, and the second step is to share! Please feel free to check out my
GitHub for code, make additions/edits, or let me know if you have
comments. That’s how we make the best available science!
Communications
AFSC RACE Groundfish and Shellfish Survey Public
Data.
- This dataset includes non-zero (presence) observations and
catch-per-unit-effort (CPUE) estimates for most identified species at a
standard set of stations in the Northern Bering Sea (NBS), Eastern
Bering Sea (EBS), Bering Sea Slope (BSS), Gulf of Alaska (GOA), and
Aleutian Islands (AI) Surveys conducted by the esource Assessment and
Conservation Engineering Division (RACE) Groundfish Assessment Program
(GAP) of the Alaska Fisheries Science Center (AFSC). There are no legal
restrictions on access to the data. The data from this dataset are
shared on the Fisheries One Stop Stop (FOSS) platform (https://www.fisheries.noaa.gov/foss/f?p=215:200:13045102793007:Mail:NO:::).
The GitHub repository for the scripts that created this code can be
found at https://github.com/afsc-gap-products/gap_public_dataThese
data were last updated NA.
- Links: GitHub of R
Package, Webpage
GAP Survey Temperature Maps.
- These scripts create the daily tempertaure and anomaly plots as NOAA
Fisheries’ Alaska Fisheries Science Center conducts fisheries
independant surveys in Alaska. The script pull temperature content from
google drive and then push the maps to google drive for the
communictions team.
- Links: GitHub
of R Package, Webpage
R Markdown Reports
Alaska Fisheries Science Center Survey Data
Reports.
- Reproducibly automate groundfish data reports for all surveys
conducted by the AFSC in R Markdown.
- Links: GitHub of
Repository
2021 Northern Bering Sea Groundfish and Crab Trawl Survey
Highlights.
- Reproducibly automate outreach reports for the Bering strait
communities with results from the northern Bering sea survey conducted
by the AFSC in R Markdown.
- Links: GitHub
of Private Repository
Fisheries Economics of the US Report.
- Manage the redevelopment and production of the Fisheries Economics
of the US report. This is a national-level report that provides ten
years of economic information, impacts, and analyses related to U.S.
commercial and recreational fishing activities and fishing-related
industries. I am working to contemporize this iconic report by writing
reproducible code using R and RMarkdown, which produces several report
outputs and JavaScript files for the interactive FEUS online tool. All
of this work has gone into improving this nationally regarded report for
the many who reference it and making the process of producing it more
streamlined, reproducible, and efficient.
- Links: Website
R Packages
{surveyIndex}: R package for calculating survey indices by
age from DATRAS exchange data..
{NMFSReports}: Easily write NOAA reports and Tech Memos in R
Markdown.
- The NMFSReports Package has all of the basic architecture you need
to create reproducible and repeatable NOAA Tech Memos in R Markdown!
This approach is perfect for efficiently rolling out annual (or other
regular) reports or reports with formulaic sections (the same chapter
structure but for a different area or species). Scripts integrate table,
figure, data, and bibliography management and design automation.
- Links: Pkgdown Site
for R Package
{FishEconProdOutput}: Measuring Output for U.S. Commercial
Fisheries From Theory to Practice.
- This package provides guidelines on fishery productivity measurement
at the individual fishery and aggregate sector levels. Attention is
given to the constructions of output and total factor productivity based
on available data and a bottom-up approach. Given that there is no
nation-wide standard cost survey, we recommend starting with measuring
TFP at the fishery level based on a translog gross output production
possibility frontier using index number techniques. Special attention is
given to measuring quality-adjusted physical capital inputs in the
bottom-up approach.
- Links: Pkgdown
Site for R Package
R Shiny Applications and Websites
AFSC RACE GAP Survey App.
- This repo uses a google spreadsheet listing content to build a
consistent, reproducible, and reliable local resource website for our
boats while boats are out to sea.
- Links: GitHub to R
Package, GitHub
to RShiny App
NOAA Fisheries Commerical, Recreational, and Aquaculture
Fisheries Economic Impact R Shiny Model.
- I/O models are used to assess economic activity such as jobs,
income, and sales generated by a given industry sector. This is
currently used in industry statistics (such as in FEUS) and management
applications (to determine how a change would effect the economy, such
as in planning team meetings).
- Links: GitHub to R
Package, GitHub to
RShiny App
NOAA Fisheries Marine Mammal Acoustic
Thresholds.
- NMFS has provided this Web Calculator as an optional tool to provide
estimated effect distances (i.e., isopleths) where PTS onset thresholds
may be exceeded. Results provided by this calculator do not represent
the entirety of the comprehensive effects analysis, but rather serve as
one tool to help evaluate the effects of a proposed action on marine
mammal hearing and make findings required by NOAA’s various statutes.
Input values are the responsibility of the individual user.
- Links: GitHub
Repository, Shiny
App
Research
Model-Based Abundance and Distribution Estimates using
VAST.
- Help provide model-based estimates of abundance, distribution, or
age composition from AFSC Groundfish Assessment Program (GAP) bottom
trawl survey data to stock assessment authors.
- Links: GitHub of
Private Repository, ModSquad

Modeling Environmentally Driven Distribution Shifts for Two
Demersal, Migratory Species.
- Habitat suitability models (HSMs) of summer flounder
(Paralichthys dentatus) and black sea bass (Centropristis
striata) were created using the fishery-independent Northeast
Fisheries Science Center (NEFSC) bottom trawl survey data in generalized
additive models and cumulative distribution functions. These analyses
were used to probabilistically link where different length classes of
these fish would likely be across different environmental variables in
spring and fall. These different environmental variables (surface and
bottom temperature and salinity, depth, and bottom type) have similar
influences on life history of these two demersal, migratory, and
commercially important species. Then, the HSMs were used to illustrate
how the population’s distribution changed over time by hindcasting over
regional ocean modeling systems (ROMS). The ROMS used in this analysis
was a 1 Day Averaged ROMS for the Northeast US Coastline from
1958-2020.
- Links: Lab
website
© Copyright 2022 Emily Markowitz